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VARAN: a web server for variability analysis of DNA microarray experiments.

G Golfier1, M Tran Dang, L Dauphinot

  • 1Neurobiologie et Diversité Cellulaire, CNRS UMR7637, Ecole Supérieure de Physique et de Chimie Industrielles, 10 rue Vauquelin, 75005 Paris, France. geoffroy.golfier@espci.fr

Bioinformatics (Oxford, England)
|February 14, 2004
PubMed
Summary

This study introduces VARAN (VARiability Analysis of DNA microarrays), a web server for analyzing DNA microarray data variability. It helps identify significant gene expression variations between experimental conditions.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • DNA microarrays are widely used for gene expression analysis.
  • Assessing variability in microarray data is crucial for reliable results.
  • Existing methods may not fully capture experimental variability.

Purpose of the Study:

  • To introduce VARAN, a novel web server for DNA microarray variability analysis.
  • To provide a tool for signal intensity-based analysis of log2 expression ratio variability.
  • To enable comparison of experimental data with a control variability model.

Main Methods:

  • Development of VARAN, a freely available web server.
  • Implementation of two modules: VARAN generator for sliding windows analysis (mean and SD) and VARAN analyzer for model comparison.
  • Inclusion of five normalization methods for intensity signals.

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Main Results:

  • VARAN computes experimental variability (mean and SD) using a sliding windows approach.
  • The analyzer module compares experimental data against a previously established asymptotic variability model.
  • The tool identifies genes with significant expression variations between conditions.

Conclusions:

  • VARAN offers a robust method for analyzing DNA microarray data variability.
  • The tool facilitates the identification of differentially expressed genes.
  • VARAN provides a valuable resource for researchers in genomics and bioinformatics.